1. Haddock (Haddock web version is fairly easy to work with.  The best thing is that you don’t need to buy a server.  However, running locally on a linux/unix machine will bring a lot of flexibility)

http://www.nmr.chem.uu.nl/haddock/

2. Autodock ( This package employs a new and efficient docking algorithm.  You can run it locally on a window or Mac machine.)

http://autodock.scripps.edu/

3. ZDOCK ( very good package if you want to perform rigid body docking)

http://zlab.umassmed.edu/zdock/index.shtml

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2 Responses to Protein-ligand docking software

  1. severse says:

    I also like GRAMM from the Vakser laboratory @ University of Kansas.

  2. Kai says:

    will give it a shot. Thanks a lot!